X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=23d04b7ab82b5f6637282d817e667d492bd3735d;hb=2ef43e1e505af2742f1c3a59619c8a4357ea82c4;hp=14363e187f0c55eca1a5535e6ce0ba8d0245e1e1;hpb=03e082a4dba4e1ba9b6929ca3d3f8055f9224fc1;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 14363e1..23d04b7 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -32,6 +32,9 @@ import java.awt.event.*;
 
 import javax.swing.*;
 
+import java.util.Vector;
+import jalview.io.FormatAdapter;
+
 
 /**
  * DOCUMENT ME!
@@ -68,14 +71,25 @@ public class PopupMenu extends JPopupMenu
     JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
     JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
     JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
-
-    /**
+  JMenu editMenu = new JMenu();
+  JMenuItem cut = new JMenuItem();
+  JMenuItem copy = new JMenuItem();
+  JMenuItem upperCase = new JMenuItem();
+  JMenuItem lowerCase = new JMenuItem();
+  JMenuItem toggle = new JMenuItem();
+  JMenu pdbMenu = new JMenu();
+  JMenuItem pdbFromFile = new JMenuItem();
+  JMenuItem enterPDB = new JMenuItem();
+  JMenuItem discoverPDB = new JMenuItem();
+  JMenu outputMenu = new JMenu();
+
+  /**
      * Creates a new PopupMenu object.
      *
      * @param ap DOCUMENT ME!
      * @param seq DOCUMENT ME!
      */
-    public PopupMenu(final AlignmentPanel ap, Sequence seq)
+    public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
     {
         ///////////////////////////////////////////////////////////
         // If this is activated from the sequence panel, the user may want to
@@ -101,6 +115,23 @@ public class PopupMenu extends JPopupMenu
         colours.add(PIDColour);
         colours.add(BLOSUM62Colour);
 
+        for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-1; i++)
+        {
+          JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
+                                         elementAt(
+                                             i));
+          item.addActionListener(new java.awt.event.ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              outputText_actionPerformed(e);
+            }
+          });
+
+          outputMenu.add(item);
+        }
+
+
         try
         {
             jbInit();
@@ -113,11 +144,15 @@ public class PopupMenu extends JPopupMenu
 
         if (seq != null)
         {
+          int start = Math.max(sequence.getName().length()-15, 0);
+          sequenceMenu.setText(sequence.getName().substring(start));
+
           JMenuItem menuItem;
           if( seq.getDatasetSequence().getPDBId() != null)
           {
             java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
                 elements();
+
             while (e.hasMoreElements())
             {
               final PDBEntry pdb = (PDBEntry) e.nextElement();
@@ -143,9 +178,10 @@ public class PopupMenu extends JPopupMenu
                   hideSequences(false);
                 }
               });
-          sequenceMenu.add(menuItem);
+          add(menuItem);
 
-          if(ap.av.getSelectionGroup() !=null && ap.av.getSelectionGroup().getSize()>1)
+          if(ap.av.getSelectionGroup() !=null
+             && ap.av.getSelectionGroup().getSize(false)>1)
           {
             menuItem = new JMenuItem("Represent Group with " + seq.getName());
             menuItem.addActionListener(new java.awt.event.ActionListener()
@@ -158,6 +194,42 @@ public class PopupMenu extends JPopupMenu
             sequenceMenu.add(menuItem);
           }
 
+          if (ap.av.hasHiddenRows)
+          {
+            final int index = ap.av.alignment.findIndex(seq);
+
+            if (ap.av.adjustForHiddenSeqs(index) -
+                ap.av.adjustForHiddenSeqs(index - 1) > 1)
+            {
+              menuItem = new JMenuItem("Reveal Sequences");
+              menuItem.addActionListener(new ActionListener()
+              {
+                public void actionPerformed(ActionEvent e)
+                {
+                  ap.av.showSequence(index);
+                  ap.repaint();
+                  if (ap.overviewPanel != null)
+                    ap.overviewPanel.updateOverviewImage();
+                }
+              });
+              add(menuItem);
+            }
+
+            menuItem = new JMenuItem("Reveal All");
+            menuItem.addActionListener(new ActionListener()
+                {
+                  public void actionPerformed(ActionEvent e)
+                  {
+                    ap.av.showAllHiddenSeqs();
+                    ap.repaint();
+                    if (ap.overviewPanel != null)
+                      ap.overviewPanel.updateOverviewImage();
+                      }
+                });
+
+            add(menuItem);
+          }
+
 
         }
 
@@ -227,38 +299,48 @@ public class PopupMenu extends JPopupMenu
             showColourText.setSelected(sg.getColourText());
             showBoxes.setSelected(sg.getDisplayBoxes());
         }
+        else
+        {
+          groupMenu.setVisible(false);
+          editMenu.setVisible(false);
+        }
 
         if (!ap.av.alignment.getGroups().contains(sg))
         {
             unGroupMenuItem.setVisible(false);
         }
-        else
-        {
-            groupMenu.insertSeparator(3);
-        }
+
 
         if (seq == null)
         {
             sequenceMenu.setVisible(false);
+            pdbMenu.setVisible(false);
         }
-        else
-        {
-          java.util.Vector links = Preferences.sequenceURLLinks;
 
+        if(links != null && links.size()>0)
+        {
           JMenu linkMenu = new JMenu("Link");
           JMenuItem item;
           for(int i=0; i<links.size(); i++)
           {
             String link = links.elementAt(i).toString();
+            final String label = link.substring(0, link.indexOf("|"));
+            item = new JMenuItem(label);
+            final String url;
 
-            item = new JMenuItem(link.substring(0, link.indexOf("|")));
-            String id = sequence.getName();
-            if(id.indexOf("|")>-1)
-              id = id.substring(id.lastIndexOf("|")+1);
-
-            final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
-                + id +
-                link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+            if (link.indexOf("$SEQUENCE_ID$") > -1)
+            {
+              String id = seq.getName();
+              if (id.indexOf("|") > -1)
+                id = id.substring(id.lastIndexOf("|") + 1);
+
+              url = link.substring(link.indexOf("|") + 1,
+                                   link.indexOf("$SEQUENCE_ID$"))
+                  + id +
+                  link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+            }
+            else
+              url = link.substring(link.lastIndexOf("|")+1);
 
 
             item.addActionListener(new java.awt.event.ActionListener()
@@ -271,7 +353,10 @@ public class PopupMenu extends JPopupMenu
 
             linkMenu.add(item);
           }
-          add(linkMenu);
+          if(sequence!=null)
+            sequenceMenu.add(linkMenu);
+          else
+            add(linkMenu);
         }
     }
 
@@ -284,7 +369,7 @@ public class PopupMenu extends JPopupMenu
     private void jbInit() throws Exception
     {
         groupMenu.setText("Group");
-        groupMenu.setText("Define");
+        groupMenu.setText("Selection");
         groupName.setText("Name");
         groupName.addActionListener(new java.awt.event.ActionListener()
             {
@@ -355,20 +440,89 @@ public class PopupMenu extends JPopupMenu
                     showColourText_actionPerformed(e);
                 }
             });
-        add(groupMenu);
-        add(sequenceMenu);
-        groupMenu.add(groupName);
-        groupMenu.addSeparator();
-        groupMenu.add(unGroupMenuItem);
+    editMenu.setText("Edit");
+    cut.setText("Cut");
+    cut.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cut_actionPerformed(e);
+      }
+    });
+    upperCase.setText("To Upper Case");
+    upperCase.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        upperCase_actionPerformed(e);
+      }
+    });
+    copy.setText("Copy");
+    copy.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        copy_actionPerformed(e);
+      }
+    });
+    lowerCase.setText("To Lower Case");
+    lowerCase.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        lowerCase_actionPerformed(e);
+      }
+    });
+    toggle.setText("Toggle Case");
+    toggle.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        toggle_actionPerformed(e);
+      }
+    });
+    pdbMenu.setText("Associate Structure with Sequence");
+    pdbFromFile.setText("From File");
+    pdbFromFile.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pdbFromFile_actionPerformed(e);
+      }
+    });
+    enterPDB.setText("Enter PDB Id");
+    enterPDB.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        enterPDB_actionPerformed(e);
+      }
+    });
+    discoverPDB.setText("Discover PDB ids");
+    discoverPDB.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        discoverPDB_actionPerformed(e);
+      }
+    });
+    outputMenu.setText("Output to Textbox...");
+    add(groupMenu);
+
+    add(sequenceMenu);
+    groupMenu.add(editMenu);
+    groupMenu.add(outputMenu);
+    groupMenu.addSeparator();
+    groupMenu.add(groupName);
+    groupMenu.add(unGroupMenuItem);
         groupMenu.add(colourMenu);
-        groupMenu.addSeparator();
-        groupMenu.add(showBoxes);
+    groupMenu.add(showBoxes);
         groupMenu.add(showText);
         groupMenu.add(showColourText);
-        groupMenu.addSeparator();
-        groupMenu.add(outline);
+    groupMenu.add(outline);
         sequenceMenu.add(sequenceName);
-        colourMenu.add(noColourmenuItem);
+    sequenceMenu.add(pdbMenu);
+    colourMenu.add(noColourmenuItem);
         colourMenu.add(clustalColour);
         colourMenu.add(BLOSUM62Colour);
         colourMenu.add(PIDColour);
@@ -406,7 +560,15 @@ public class PopupMenu extends JPopupMenu
         colourMenu.addSeparator();
         colourMenu.add(abovePIDColour);
         colourMenu.add(conservationMenuItem);
-        noColourmenuItem.setText("None");
+    editMenu.add(copy);
+    editMenu.add(cut);
+    editMenu.add(upperCase);
+    editMenu.add(lowerCase);
+    editMenu.add(toggle);
+    pdbMenu.add(pdbFromFile);
+    pdbMenu.add(enterPDB);
+    pdbMenu.add(discoverPDB);
+    noColourmenuItem.setText("None");
         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
             {
                 public void actionPerformed(ActionEvent e)
@@ -540,7 +702,7 @@ public class PopupMenu extends JPopupMenu
     protected void clustalColour_actionPerformed(ActionEvent e)
     {
         SequenceGroup sg = getGroup();
-        sg.cs = new ClustalxColourScheme(sg.sequences,
+        sg.cs = new ClustalxColourScheme(sg.getSequences(true),
                 ap.av.alignment.getWidth());
         refresh();
     }
@@ -646,7 +808,8 @@ public class PopupMenu extends JPopupMenu
 
         if (abovePIDColour.isSelected())
         {
-            sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+            sg.cs.setConsensus(AAFrequency.calculate(
+                    sg.getSequences(true), 0,
                     ap.av.alignment.getWidth()));
 
             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
@@ -692,7 +855,7 @@ public class PopupMenu extends JPopupMenu
     {
         SequenceGroup sg = getGroup();
         sg.cs = new PIDColourScheme();
-        sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
                 ap.av.alignment.getWidth()));
         refresh();
     }
@@ -708,7 +871,7 @@ public class PopupMenu extends JPopupMenu
 
         sg.cs = new Blosum62ColourScheme();
 
-        sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
                 ap.av.alignment.getWidth()));
 
         refresh();
@@ -739,7 +902,8 @@ public class PopupMenu extends JPopupMenu
         if (conservationMenuItem.isSelected())
         {
             Conservation c = new Conservation("Group",
-                    ResidueProperties.propHash, 3, sg.sequences, 0,
+                    ResidueProperties.propHash, 3,
+                    sg.getSequences(true), 0,
                     ap.av.alignment.getWidth());
 
             c.calculate();
@@ -794,9 +958,9 @@ public class PopupMenu extends JPopupMenu
         SequenceGroup sg = getGroup();
         StringBuffer sb = new StringBuffer();
 
-        for (int i = 0; i < sg.sequences.size(); i++)
+        for (int i = 0; i < sg.getSize(false); i++)
         {
-            Sequence tmp = (Sequence) sg.sequences.get(i);
+            Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);
             sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
             sb.append("\n");
         }
@@ -963,14 +1127,14 @@ public class PopupMenu extends JPopupMenu
     void hideSequences(boolean representGroup)
     {
       SequenceGroup sg = ap.av.getSelectionGroup();
-      if(sg==null || sg.getSize()<1)
+      if(sg==null || sg.getSize(false)<1)
       {
         ap.av.hideSequence(sequence);
         return;
       }
 
         int index = 0;
-        while(index < sg.sequences.size())
+        while(index < sg.getSize(false))
         {
           if(representGroup && sg.getSequenceAt(index)!=sequence)
           {
@@ -985,7 +1149,162 @@ public class PopupMenu extends JPopupMenu
         }
 
         ap.av.setSelectionGroup(null);
+        ap.repaint();
         refresh();
     }
 
+  public void copy_actionPerformed(ActionEvent e)
+  {
+    ap.alignFrame.copy_actionPerformed(null);
+  }
+
+  public void cut_actionPerformed(ActionEvent e)
+  {
+    ap.alignFrame.cut_actionPerformed(null);
+  }
+
+  public void upperCase_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if(sg==null)
+      return;
+
+    for(int g=0; g<sg.getSize(true); g++)
+    {
+    ( (SequenceI)sg.getSequences(true).elementAt(g))
+        .changeCase(true, sg.getStartRes(), sg.getEndRes()+1);
+    }
+    ap.repaint();
+  }
+
+  public void lowerCase_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if(sg==null)
+      return;
+
+    for(int g=0; g<sg.getSize(true); g++)
+    {
+       ( (SequenceI)sg.getSequences(true).elementAt(g))
+           .changeCase(false, sg.getStartRes(), sg.getEndRes()+1);
+    }
+    ap.repaint();
+  }
+
+  public void toggle_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if (sg == null)
+      return;
+
+    for (int g = 0; g < sg.getSize(true); g++)
+    {
+      ( (SequenceI)sg.getSequences(true).elementAt(g))
+          .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
+    }
+
+    ap.repaint();
+  }
+
+  public void outputText_actionPerformed(ActionEvent e)
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    Desktop.addInternalFrame(cap,
+                             "Alignment output - " + e.getActionCommand(), 600,
+                             500);
+
+    String [] omitHidden = null;
+
+    if(ap.av.hasHiddenColumns)
+    {
+      System.out.println("PROMPT USER HERE");
+      omitHidden = ap.av.getViewAsString(true);
+    }
+
+    cap.setText(new FormatAdapter().formatSequences(
+        e.getActionCommand(),
+        ap.av.getSelectionAsNewSequence(),
+        omitHidden));
+  }
+
+
+  public void pdbFromFile_actionPerformed(ActionEvent e)
+  {
+     jalview.io.JalviewFileChooser chooser
+         = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
+         getProperty(
+             "LAST_DIRECTORY"));
+     chooser.setFileView(new jalview.io.JalviewFileView());
+     chooser.setDialogTitle("Select a PDB file");
+     chooser.setToolTipText("Load a PDB file");
+
+     int value = chooser.showOpenDialog(null);
+
+     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+     {
+       PDBEntry entry = new PDBEntry();
+       String choice = chooser.getSelectedFile().getPath();
+       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+       try
+       {
+         MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
+                                       jalview.io.AppletFormatAdapter.FILE);
+
+         if (pdbfile.id == null)
+         {
+           String reply = JOptionPane.showInternalInputDialog(
+               Desktop.desktop,
+               "Couldn't find a PDB id in the file supplied."
+               + "Please enter an Id to identify this structure.",
+               "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
+           if (reply == null)
+             return;
+
+           entry.setId(reply);
+         }
+         else
+           entry.setId(pdbfile.id);
+       }
+       catch (java.io.IOException ex)
+       {
+         ex.printStackTrace();
+       }
+
+       entry.setFile(choice);
+       sequence.getDatasetSequence().addPDBId(entry);
+     }
+
+  }
+
+  public void enterPDB_actionPerformed(ActionEvent e)
+  {
+    int size = (ap.av.getSelectionGroup() == null ? 0 :
+                ap.av.getSelectionGroup().getSize(false));
+
+    if (size == 0 || size > 1)
+    {
+      JOptionPane.showInternalMessageDialog(
+          Desktop.desktop,
+          "Select a single sequence to specify a PDB id for first",
+          "Select Single Selected", JOptionPane.WARNING_MESSAGE);
+      return;
+    }
+
+    String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
+        "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
+
+    if (id != null && id.length() > 0)
+    {
+      PDBEntry entry = new PDBEntry();
+      entry.setId(id);
+      ap.av.getSelectionGroup().getSequenceAt(0).getDatasetSequence()
+          .addPDBId(entry);
+    }
+  }
+
+  public void discoverPDB_actionPerformed(ActionEvent e)
+  {
+    new jalview.io.DBRefFetcher(
+             ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
+  }
 }